This is something that should take a couple of seconds at most. Two hours implies something seriously dysfuntional.
Could you start with checking that you've got compatible versions of Jira, Java and ANY plugins you've added. Check the amount of memory is enough for the system. Then check the logs again for *anything* it might have been doing druing those two hours. What was the cpu/disk/memory usage like during that time?
As well as the Atlassian-jira.log, check catalina.out
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